Figure 7

CHIKV RNA in the dLN localizes to MARCO+ LECs. WT C57BL/6 mice were mock-inoculated (n = 3) or inoculated with 103 PFU of CHIKV (n = 3) in the left rear footpad. At 24 hpi, the draining popliteal LN was collected and enzymatically digested into a single cell suspension. Cells were enriched for CD45- cells and analyzed by scRNA-seq as described in the materials and methods. P-values were calculated using a two-sided Wilcoxon rank-sum test with Bonferroni correction.

  1. UMAP projection shows each replicate for mock- and CHIKV-infected mice, and the number of cells obtained for each replicate is shown at the bottom for mock- and CHIKV-infected mice.
  2. UMAP projection shows annotated cell types (top) and the proportion of cells identified for each cell type (bottom).
  3. UMAP projection shows LEC endothelial subtypes (top) and the proportion of cells identified for each cell type (bottom) identified for each replicate. Non-endothelial cells are shown in white. The proportion of cells identified for each subtype is shown at the bottom.
  4. UMAP projection shows Marco expression.
  5. UMAP projection shows the fraction of counts that align to the CHIKV genome.
  6. UMAP projection shows cell types for cells classified as CHIKV-high. CHIKV-low cells are shown in white. The proportion of CHIKV-high cells belonging to each cell type is shown on the right left. for each biological replicate. Most CHIKV-high cells were identified as MACRO+ LECs or belong to a cluster of unassigned endothelial cells LECs (unassigned-LEC).
  7. The fraction of counts that align to the CHIKV genome is shown for CHIKV-high cells. Only cell types that include >20 cells are shown. MARCO+ LECs and a group of unassigned LECs endothelial cells (unassigned-LEC) show the highest viral burden.
  8. MARCO expression is shown for MARCO+ LECs for mock-infected cells and CHIKV-infected cells classified as either CHIKV-low or CHIKV-high.
  9. Mxra8 expression is shown for MARCO+ LECs for mock-infected cells and CHIKV-infected cells classified as either CHIKV-low or CHIKV-high.


Figure S6

LEC Annotations. To assess the accuracy of endothelial cell type annotations, the subtype assignments were compared back to the reference data. The correlation with the reference RNA-seq data is shown for each subtype. Correlation coefficients (Spearman) are shown for each subtype.


Figure S7

Identification of CHIKV-high cells. To identify cells harboring viral RNA, cells were first filtered to only include those with >5 CHIKV counts. K-means clustering was then used to independently group each biological replicate into CHIKV-low and CHIKV-high populations. Cells with 5 CHIKV counts or less were included in the CHIKV-low group. CHIKV counts are shown for all captured cells.


Figure S8

Expressed mouse genes in CHIKV-low and CHIKV-high cells. Cell quality metrics are shown for all captured cells. CHIKV-high cells have fewer expressed mouse genes, fewer mouse gene counts, and a higher percentage of mitochondrial counts.


Figure S?? v1

Mxra8 expression is shown for unassigned LECs for mock-infected cells and CHIKV-infected cells classified as either CHIKV-low or CHIKV-high.


Figure S?? v2

Mxra8 expression by each cell type is shown for each biological replicate.


Figure S?? v3

Mxra8 expression by each cell type is shown for mock- and CHIKV-infected samples.